The future development of quantum computing threatens a host of modern cryptographic security efforts, and thus presents a new security threat to wireless communications systems. Encryption algorithms for aeronautical mobile telemetry (AMT) may likewise be vulnerable to quantum attacks based on Grover and Simons’ algorithms. Post-quantum cryptography focuses on developing appropriate cryptographic algorithms that are impervious to both quantum and classical attacks and can therefore provide data confidentiality in a post-quantum computing world. This paper proposes the application of post-quantum cryptography as a future security solution in AMT systems with a focus on code-based techniques and provides a road map for studying the next generation of cryptosystem in AMT. We further suggest and analyzed (in terms of secrecy) the use of the McEliece cipher as a special case of a code-based post-quantum cryptographic solution for the integrated Network Enhanced Telemetry (iNET) communications system and show how it may be deployed.